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@PathologyDataScience

Computational and Integrative Pathology

Organization for the Computational and Integrative Pathology Group at Northwestern University

Popular repositories

  1. BCSS BCSS Public

    Use this to download all elements of the BCSS dataset described in: Amgad M, Elfandy H, ..., Gutman DA, Cooper LAD. Structured crowdsourcing enables convolutional segmentation of histology images. …

    Python 126 17

  2. SurvivalNet SurvivalNet Public

    Deep learning survival models

    Python 112 45

  3. SCNN SCNN Public

    Survival Convolutional Neural Networks

    66 19

  4. NuCLS NuCLS Public

    NuCLS: A scalable crowdsourcing, deep learning approach and dataset for nucleus classification, localization and segmentation

    Jupyter Notebook 43 14

  5. HistomicsML2 HistomicsML2 Public

    A tool for training machine-learning models with whole-slide imaging datasets

    JavaScript 20 4

  6. HistomicsML HistomicsML Public

    An interactive machine learning framework for large histopathology images.

    JavaScript 19 5

Repositories

Showing 10 of 19 repositories
  • HiPS Public

    Histomic Prognostic Signature (HiPS): A population-level computational histologic signature for invasive breast cancer prognosis

    Python 15 MIT 3 0 0 Updated Apr 9, 2024
  • glimr Public

    A simplified wrapper for hyperparameter search with Ray Tune.

    Python 1 Apache-2.0 0 9 0 Updated Jan 22, 2024
  • HistomicsML2 Public

    A tool for training machine-learning models with whole-slide imaging datasets

    JavaScript 20 4 10 0 Updated Dec 27, 2023
  • HistomicsML Public

    An interactive machine learning framework for large histopathology images.

    JavaScript 19 5 2 0 Updated Dec 27, 2023
  • MuTILs_Panoptic Public

    Amgad M, Salgado R, Cooper LA. A panoptic segmentation approach for tumor-infiltrating lymphocyte assessment: development of the MuTILs model and PanopTILs dataset. medRxiv 2022.01.08.22268814.

    Python 7 MIT 1 2 0 Updated May 19, 2023
  • SCNN Public

    Survival Convolutional Neural Networks

    66 19 6 1 Updated Apr 2, 2023
  • SurvivalNet Public

    Deep learning survival models

    Python 112 Apache-2.0 45 10 3 Updated Dec 27, 2022
  • MiscSurvivalUtils Public

    Miscellaneous tools for data management and classical survival analysis.

    Python 3 0 0 0 Updated Dec 10, 2022
  • NuCLS Public

    NuCLS: A scalable crowdsourcing, deep learning approach and dataset for nucleus classification, localization and segmentation

    Jupyter Notebook 43 MIT 14 3 0 Updated Apr 4, 2022
  • BCSS Public

    Use this to download all elements of the BCSS dataset described in: Amgad M, Elfandy H, ..., Gutman DA, Cooper LAD. Structured crowdsourcing enables convolutional segmentation of histology images. Bioinformatics. 2019. doi: 10.1093/bioinformatics/btz083

    Python 126 MIT 17 3 0 Updated Apr 1, 2022
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